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#!/usr/bin/perl
#---
# Initialize parameters
#---
$sampleStart = $ARGV[0];
$sampleEnd = $ARGV[1];
if(( $ARGV[0] eq '' ) || ($ARGV[1] eq '')) { die "Usage: fastaSample sampleStart sampleEnd\n"; }
$sampleStart--;
$sampleEnd--;
$sampleLen = $sampleEnd - $sampleStart + 1;
#---
# Read fasta file
#---
for($lineNum=0 ; $l = <STDIN> ; $lineNum++ ) {
if( $l =~/^>/ ) {
# Sample if not empty
if( $seq ne "" ) {
$s = substr( $seq, $sampleStart, $sampleLen);
print "$s\n";
}
# New sequence
$seq = "";
} else {
chomp($l);
$seq .= $l;
}
}
# Sample if not empty
if( $seq ne "" ) {
$s = substr( $seq, $sampleStart, $sampleLen);
print "$s\n";
}
$len = length($seq);
print STDERR "Lines: $lineNum\n";
print STDERR "Sequence size: $len\n";
print STDERR "Sample size: $sampleLen\n";
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